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This is an example showing example shows a sample report table, trial design, and results data of Study #123 dataset for study 123 for the determination of the in vitro genotoxicity potential of 10 tobacco products in using the in vitro Micronucleus Assay

Info
  • red font - indicates potential for CT code lists
  • green font - links to other domains

micronucleus assay.

Expand
titleSample Report Table for Study 123

Image Added

Dataset wrap
Rowcaps
Rows 1-2:Show 2 records for TSPARMCD = "GLPTYP", using TSSEQ to indicate multiple records, since both GLP types apply for this example study. 
Row 3:Shows that this study was conducted as a GLP study.
Rows 4-5:Show the study start date and study title.
Rows 6-7:Show the version of SEND Implementation Guide and version of Controlled Terminology used in this study.
Row 8:Shows the applicant's organization.
Row 9:Shows that the applicant's study reference ID is not applicable.
Rows 10-13:Show that TSGRPID has been used to link records (name, location, country) related to the test facility (TSGRPID = 1). The study director is associated with the test facility.
Rows 14-16:

Show that TSGRPID (TSGRPID=2) has been used to link the information on the testing guideline followed on this study (TSTGDNAM, TSTGDORG, TSTGDVER).

Row 17:

Shows the study type for this study.

Row 18:

Shows that this study includes a Mammalian Cell Micronucleus Assay.
Rows 19-20:Show that the species is human and the cell line is TK6 lymphoblastoid in this study.
Expand
titlets.xpt (trial summary, study level parameters)
  • Assumption: A Trial (study) can have more than one assay type
  • Assumption: ASSAYID value of ALL indicates that it applies to all assays in the study
  • BLEO & CPA - are positive controls, should this be included/where is this captured? — in results for the record / row?
  • Where is TK6 cell type?  is this test system (see below)
    • needs to be allowed to vary down to the well level / result level
  • For the items highlighted in orange - what is the lowest level where this could vary?  e.g. at the level of a well in a 96-well plate, or a slide vs. assay level vs. product level
    • Smoke Regime needs to be allowed to vary down to the well level / result level
    • run - also at result level 
    • port - (smoking product on the machine, you assign a run number or port-number for multiple replicates depending on linear vs. rotary machines; machine bias), needs to be allowed to vary down to the well level / result level)
    • replicate - (e.g., multiple samples from one vial), could be a replicate per exposure (e.g., 3 plates, multiple analyses for exposure)
    • sample ID - typically a unique number assigned (at CRO) or supplied by sponsor - result level
    • Smoke fraction - result level (e.g.tpm particulate vs. gas gvp)

Row

STUDYID

ASSAYID
Dataset2
Row

STUDYID

DOMAIN

TSSEQ

TSGRPID

TSPARMCD

TSPARM

TSVAL

TSVALNF

1123
ALL
TS1
GLPTYPGood Laboratory Practice TypeFDA
2123
ALL
TS2
GLPTYPGood Laboratory Practice TypeOECD
3123
TS1
GLPFLGLP FlagY
4123
ALL
TS1
STSTDTCStudy Start Date2022-05-25
4

5123
ALL
TS1
STITLEStudy Title

Determination of the in vitro genotoxicity potential

of 10 tobacco products in both the in vitro Micronucleus Assay and the in vitro Neutral Red Uptake

using the in vitro Neutral Red Uptake assay


6123
5123ALL
TS1
SNDIGVERSEND Implementation Guide VersionTOBACCO IMPLEMENTATION GUIDE VERSION 1.0
6

7123

ALL

TS1
SNDCTVERSEND Controlled Terminology VersionSEND Terminology 2021-09-30
7

8123
ALL
TS1
SSPONSOR

APPLCNT
Sponsor Organization

Applicant

Example
Sponsor
Applicant, Inc.
8

9123
ALL
TS1
SPREFID

APREFID
Sponsor's
Study Reference ID
NOT APPLICABLE
9
10123
ALL
TS11TSTFNAMTest Facility NameExample
Tox
Test Lab Name
10

11123
ALL
TS11TSTFLOCTest Facility Location10 Somewhere Street, Montgomery, AL 10000
11

12123
ALL
TS11TFCNTRYTest Facility CountryUSA
...

13123
ALL
TS11STDIRStudy DirectorDr. R. Smith
14123
ALL
TS1
GLPFLGLP FlagY123
2TSTGDNAMTesting Guideline NameGUIDELINE FOR THE TESTING OF CHEMICALS No. 487
15123
MNvit
TS1
ASTDAssay Standard
2TSTGDORGTesting Guideline OrganizationOECD
16
OECD Test No. 487 
123
MNvit
TS1
ASTDV
2TSTGDVERTesting Guideline
Assay Standard
Version
2016
29-
07
July-
29
2016
17123
MNvit
TS1
SSTYPStudy TypeGENOTOXICITY IN VITRO
18123
MNvit
TS1
SSSTYPStudy Sub TypeIn Vitro Micronucleus

GNTXAIDGenetic Toxicology Assay IdentifierMNvit
19123
123MNvit
TS1
SPECIESSpeciesHUMAN
Homo Sapiens

20123
MNvit
TS1
??Test System?

CELLLNCell Line

TK6

Lymphoblastoid Suspension Cells123NRUTS1ASTDAssay StandardNIH Publication No. 07-4519123NRUTS1ASTDVAssay Standard Version2006-11123NRUTS1SSTYPStudy TypeGENOTOXICITY IN VITRO123NRUTS1SSSTYPStudy Sub TypeIn Vitro Neutral Red Uptake123NRUTS1SPECIESSpeciesSalmonella enterica 123NRUTS1STRAINStrain/SubstrainSalmonella enterica enterica123NRUTS1??Test System??Normal Human Keratinocyte123NRUTS1REGIMESmoking RegimeTraditional combustible 123NRUTS1RUNPRTrun-port number?? (always same for whole assay?)

1-1

123NRUTS1SMPLIDSample ID030001123NRUTS1SMKFRCSmoke FractionA123NRUTS1REPNUMReplicate Number1 Expand
titletx.xpt (trial sets)
  • During CT definition/reviews will decide appropriate TXPARM and TXVAL; Treatment duration may be controlled;  For now, we just include good example values based on our experience
  • Assumption: The Trial Sets (TX) domain provides the list of distinct sets of subjects having different experimental factors, treatment factors, inherent characteristics, or distinct sponsor designations as specified in the trial design.
RowSTUDYIDASSAYIDDOMAINSETCD
SET (what sponsor calls it)
TXSEQTXPARMCDTXPARMTXVAL1123NRUTX1-1-A
(plate-col-row in the 96-well plate)
CSC-10
(through SLS-200)
PLATENUM. (e.g., 1 or 2)
12123NRUTX1-1-ACSC-10
WELLNUM (e.g., 1-A through 10-H)
Number representing the location of the well in the 96-well plate1-A 3123NRUTX1-1-ACSC-10INTRVNname of the intervention articleCigarette Smoke Condensate4123NRUTX1-1-ACSC-10ITVTYPE
(CT e.g, Product, positive control, negative control)
type of intervention articlePRODUCT5123NRUTX1-1-ACSC-10ITVCONCintervention concentration106123NRUTX1-1-ACSC-10ITVCONCUintervention unitug/ml7123NRUTX1-1-BCSC-10PLATENUMPlate number1  8123NRUTX1-1-BCSC-10WELLNUMNumber representing the location of the well in the 96-well plate2-A 9123NRUTX1-1-BCSC-10INTRVNname of the intervention articleCigarette Smoke Condensate10123NRUTX1-1-BCSC-10ITVTYPEtype of intervention articlePRODUCT11123NRUTX1-1-BCSC-10ITVCONCintervention concentration1012123NRUTX1-1-BCSC-10ITVCONCUintervention unitug/ml......123NRUTX1-10-HSLS-10PLATENUMPlate number1  123NRUTX1-10-HSLS-10WELLNUMNumber representing the location of the well in the 96-well plate10-H123NRUTX1-10-HSLS-10INTRVNname of the intervention articlesodium laurel sulfate123NRUTX1-10-HSLS-10ITVTYPEtype of intervention articlePOSITIVE CONTROL123NRUTX1-10-HSLS-10ITVCONCintervention concentration200123NRUTX1-10-HSLS-10ITVCONCUintervention unitug/ml......123NRUTX2-10-HSLS-10PLATENUMPlate number2123NRUTX2-10-HSLS-10WELLNUMNumber representing the location of the well in the 96-well plate10-H123NRUTX2-10-HSLS-10INTRVNname of the intervention articlesodium laurel sulfate123NRUTX2-10-HSLS-10ITVTYPEtype of intervention articlePOSITIVE CONTROL123NRUTX2-10-HSLS-10ITVCONCintervention concentration200123NRUTX2-10-HSLS-10ITVCONCUintervention unitug/ml123MNvitTXA1METACTMetabolic Activation  (should there be two parms? Presence, type)?+S9123MNvitTXA1TRTDRTRGTreatment Duration target. (how do we show 3-6 hour range?  start/end, target and tolerance?, one text field not-analyzable)3123MNvitTX123MNvitTXTRTDRTOLTreatment Duration Tolerance123MNvitTXTRTDURUTreatment Duration Unit (this is for both TRTDURT, TRTDURTOL)H123MNvitTXINTRVNname of the intervention articleBleomycin or Cyclophosphamid A123MNvitTXITVTYPEtype of intervention articlechoices of values:  product; negative control; positive control123MNvitTXA1ITVCONCConcentration of i a 0123MNvitTXA1ITVCONCUConcentration Unitug/ml Expand
titlegt.xpt (similar to LB)

Image RemovedImage Removed

RowSTUDYIDASSAYIDDOMAINTXCDGTSEQGTTESTCDGTTESTGTCELLEV
(cells evaluated)GTORRESGTORRESUGTSTRESCGTSTRESNGTSTRESUGTDTCGTNOMDYGTELTMGTTPTREF1123NRUGT1-1-A1RELABSRelative Absorbance Reading100ug/ml100100ug/ml2123NRUGT1-1-B1RELABSRelative Absorbance Reading107ug/ml100100ug/ml3123NRUGT1-1-C1RELABSRelative Absorbance Reading98.6ug/ml100100ug/ml54123NRUGT1-1-D1RELABSRelative Absorbance Reading94.9ug/ml100100ug/ml6123NRUGT1-1-E1RELABSRelative Absorbance Reading1117123NRUGT1-1-F1RELABSRelative Absorbance Reading96.98123NRUGT1-1-G1RELABSRelative Absorbance Reading1059123NRUGT1-1-H1RELABSRelative Absorbance Reading95.210123NRUGT1-2-A1RELABSRelative Absorbance Reading

83.0

11123NRUGT1-2-B1RELABSRelative Absorbance Reading77.7......80123NRUGT1-10-H1RELABSRelative Absorbance Reading0.791......160123NRUGT2-10-H1RELABSRelative Absorbance Reading0.7801123MNvitGTA21RICCRelative Increase in Cell Count13415.7%15.715.7%2022-05-252123MNvitGTA22RCCRelative Cell Count13413.0%13.013.0%2022-05-253123MNvitGTA23RPDRelative Population Doubling1347.9%7.97.9%2022-05-254123MNvitGTA24MNCELLSMicronucleated Cells326620Cells2020Cells2022-05-255123MNvitGTA25MNCELLSMicronucleated Cells219017Cells1717Cells2022-05-256123MNvitGTA26MNCELLSMicronucleated Cells275813Cells1313Cells2022-05-257123MNvitGTA27MNCELLSMicronucleated Cells271421Cells2121Cells2022-05-258123MNvitGTA28AVGRELAverage Relative MN Frequency0.66%0.660.66%2022-05-259123MNvitGTA11RICCRelative Increase in Cell Count1540%00%2022-05-2510123MNvitGTA12RCCRelative Cell Count1540%00%2022-05-2511123MNvitGTA13RPDRelative Population Doubling1540%00%2022-05-2512123MNvitGTA14MNCELLSMicronucleated Cells326615Cells1515Cells2022-05-2513123MNvitGTA15MNCELLSMicronucleated Cells219013Cells1313Cells2022-05-2514123MNvitGTA16MNCELLSMicronucleated Cells275817Cells1717Cells2022-05-2515123MNvitGTA17MNCELLSMicronucleated Cells271412Cells1212Cells2022-05-2516123MNvitGTA18AVGRELAverage Relative MN Frequency0.57%0.570.57%2022-05-25

Below this line are domains we currently do not see a use for

LYMPHOBLASTOID


This example Trial Sets dataset shows information about the test conditions for set A1 and A2 in this example study. Sets A1 and A2 can be seen in the first and second rows respectively of the sample report Table 1 (above). For brevity, the TX dataset and the findings (GT) dataset do not show information for any other sets. Fully formed datasets for this example study would include information about the test conditions and findings for all sets. 

Dataset wrap
Nametx
Rowcaps
Rows 1-23:

Show trial set parameters and values that comprise the test conditions for trial set A1. Set A1 is the data for the negative control (concentration 0) with short-term exposure and metabolic activation S9.  The applicant has chosen to given a long name (SET) equal to "ST+S9_C0".

Set A1 is associated with the first row in the sample report table for study 123.

Rows 24-46:

Show trial set parameters and values that comprise the test conditions for trial set A2. Set A2 is the data for the short-term exposure with metabolic activation S9 at a concentration of 1250 ug/ml. The applicant has chosen to give the set a long name (SET) equal to "ST+S9_C1250".

Set A2 is associated with the second row in the sample report table for study 123.

Dataset2
RowSTUDYIDDOMAINSETCDSETTXSEQTXPARMCDTXPARMTXVAL
1123TXA1ST+S9_C01MTACTINDMetabolic Activating Agent Name+S9
2123TXA1ST+S9_C02METACTFLPresence of Metabolic Activation FlagY
3123TXA1ST+S9_C03

IVTDMIN

In vitro Treatment Duration Minimum3
4123TXA1ST+S9_C04IVTDTRGIn vitro Treatment Duration Target3.5
5123TXA1ST+S9_C05IVTDMAXIn vitro Treatment Duration Maximum4
6123TXA1ST+S9_C06IVTDUIn vitro Treatment Duration UnitHOURS
7123TXA1ST+S9_C07RCVDMINRecovery Duration Minimum23.5
8123TXA1ST+S9_C08RCVDTRGRecovery Duration Target24
9123TXA1ST+S9_C09RCVDMAXRecovery Duration Maximum24.5
10123TXA1ST+S9_C010RCVDURecovery Duration UnitHOURS
11123TXA1ST+S9_C011INCBTMPIncubation Temperature37
12123TXA1ST+S9_C012INCBTMPUIncubation Temperature UnitC
13123TXA1ST+S9_C013ATMRHPAtmospheric Relative Humidity Percent50
14123TXA1ST+S9_C014ATMCO2PAtmospheric CO2 Percent5
15123TXA1ST+S9_C015

SPTOBID

Applicant-defined tobacco identifier

CIG01a
16123TXA1ST+S9_C016EXPTYP

Exposure Type

Submerged
17123TXA1ST+S9_C017SAMTYP

Sample Type

Total Particulate Matter in DMSO
18123TXA1ST+S9_CO18ITVNAM

Intervention Article Name

Tobacco ProdA
19123TXA1ST+S9_C019ITVTYPE

Intervention Article Type

Negative Control
20123TXA1ST+S9_C020ITVCONCIntervention Article Concentration0
21123TXA1ST+S9_C021ITVCONCUIntervention Article Concentration Unitug/ml
22123TXA1ST+S9_C022

SPDEVID

Applicant-defined device identifierPUFFMASTER3K
23123TXA1ST+S9_C023

SMKRGM

Smoking RegimenMEDIUM INTENSITY REGIMEN
24123TXA2ST+S9_C125024MTACTINDMetabolic Activating Agent Name+S9
25123TXA2ST+S9_C125025METACTFLPresence of Metabolic Activation FlagY
26123TXA2ST+S9_C125026

IVTDMIN

In vitro Treatment Duration Minimum3
27123TXA2ST+S9_C125027IVTDTRGIn vitro Treatment Duration Target3.5
28123TXA2ST+S9_C125028IVTDMAXIn vitro Treatment Duration Maximum4
29123TXA2ST+S9_C125029IVTDUIn vitro Treatment Duration UnitHOURS
30123TXA2ST+S9_C125030RCVDMINRecovery Duration Minimum23.5
31123TXA2ST+S9_C125031RCVDTRGRecovery Duration Target24
32123TXA2ST+S9_C125032RCVDMAXRecovery Duration Maximum24.5
33123TXA2ST+S9_C125033RCVDURecovery Duration UnitHOURS
34123TXA2ST+S9_C125034INCBTMPIncubation Temperature37
35123TXA2ST+S9_C125035INCBTMPUIncubation Temperature UnitC
36123TXA2ST+S9_C125036ATMRHPAtmospheric Relative Humidity Percent50
37123TXA2ST+S9_C125037ATMCO2PAtmospheric CO2 Percent5
38123TXA2ST+S9_C125038

SPTOBID

Applicant-defined tobacco identifier

CIG01a
39123TXA2ST+S9_C125039EXPTYP

Exposure Type

Submerged
40123TXA2ST+S9_C125040SAMTYP

Sample Type

Total Particulate Matter in DMSO
41123TXA2ST+S9_C125041ITVNAM

Intervention Article Name

Tobacco ProdA
42123TXA2ST+S9_C125042ITVTYPE

Intervention Article Type

Product
43123TXA2ST+S9_C125043ITVCONCIntervention Article Concentration1250
44123TXA2ST+S9_C125044ITVCONCUIntervention Article Concentration Unitug/ml
45123TXA2ST+S9_C125045SPDEVIDApplicant-defined Device IdentifierPUFFMASTER2023
46123TXA2ST+S9_C125046

SMKRGM

Smoking RegimenHIGH INTENSITY REGIMEN
Dataset wrap
Namerelref
Rowcaps
Row 1:Shows the value of REFID=C0. This REFID refers to the trial set with a SETCD of "A1", as defined in the TX dataset. LEVEL=1 and LVLDESC="EXPERIMENTAL UNIT/TRIAL SET" indicates this identifier is referring to both the experimental unit and the unit to which the treatment is applied, and to the entire trial set.
Rows 2-5:Show the values of 4 observational units (C0_Count1 through C0_Count4) that are within the parent experimental unit, REFID=C0. In this example assay, these observational units are also all within the same trial set, as defined in the TX dataset.
Row 6:Shows the value of REFID=C1250. This REFID refers to the trial set with a SETCD of "A2", as defined in the TX dataset. LEVEL=1 and LVLDESC="EXPERIMENTAL UNIT/TRIAL SET" indicates this identifier is referring to both the experimental unit and the unit to which the treatment is applied, and to the entire trial set.
Rows 7-10:

Show the values of 4 observational units (C1250_Count1 through C1250_Count4) that are within the parent experimental unit, REFID=C1250. In this example assay, these observational units are also all within the same trial set, as defined in the TX dataset.

Dataset2
tableidrelref

Row

STUDYID

SETCD

REFID

PARENT

LEVEL

LVLDESC

1

123

A1

C0
1

EXPERIMENTAL UNIT/TRIAL SET

2

123

A1

C0-Count1C02OBSERVATIONAL UNIT

3

123

A1

C0-Count2C02OBSERVATIONAL UNIT

4

123

A1

C0-Count3C02OBSERVATIONAL UNIT

5

123

A1

C0-Count4C02OBSERVATIONAL UNIT

6

123A2C1250
1EXPERIMENTAL UNIT/TRIAL SET
7123A2C1250-Count1C12502OBSERVATIONAL UNIT
8123A2C1250-Count2C12502OBSERVATIONAL UNIT
9123A2C1250-Count3C12502OBSERVATIONAL UNIT
10123A2C1250-Count4C12502OBSERVATIONAL UNIT

(Do we need this? a single element (treatment)?)

(Do we need this? one arm for each trial set?)

ARMCD
Dataset wrap
Namegt
Rowcaps

Rows 1-3, 8:

Show percentage result values that apply to GTREFID=C0. REFID=C0, as shown in the RELREF dataset, relates this data to the trial set in the first row of table 1 in the sample report table for study 123.
Rows 4-7:Show the 4 micronucleated cell counts for the observational units with GTREFID from C0-Count1 through C0-Count4, for which their relationship to test conditions (in tx.xpt) and experimental units (in relref.xpt) are shown in the RELREF dataset.

Rows 9-11, 16:

Show percentage result values that apply to GTREFID=C1250. REFID=C1250, as shown in the RELREF dataset, relates this data to the trial set in the second row of table 1 in the sample report table for study 123.
Rows 12-15:Show the 4 micronucleated cell counts for the observational units with GTREFID from C1250-Count1 through C1250-Count4, for which their relationship to test conditions (in tx.xpt) and experimental units (in relref.xpt) are shown in the RELREF dataset.
Dataset2
RowSTUDYIDDOMAINGTSEQ

GTREFID

GTTESTCDGTTESTGTCELLEVGTORRESGTORRESU

GTCOLSRT

GTSTRESCGTSTRESNGTSTRESUGTDTC
1123GT1C0

RICC

Relative Increase in Cell Count1540%
00%2022-05-25
2123GT2C0RCCRelative Cell Count1540%
00%2022-05-25
3123GT3C0RPDRelative Population Doubling1540%
00%2022-05-25
4123GT4C0-Count1MNCEMicronucleated Cells220515



1515
2022-05-25
5123GT5C0-Count2MNCEMicronucleated Cells247413

1313
2022-05-25
6123GT6C0-Count3MNCEMicronucleated Cells275817

1717
2022-05-25
7123GT7C0-Count4MNCEMicronucleated Cells266912

1212
2022-05-25
8123GT8C0MNCECEMicronucleated Cells/Total Cells
0.57%
0.570.57%2022-05-25
9123GT1C1250RICCRelative Increase in Cell Count13415.7%
15.715.7%2022-05-25
10123GT2C1250RCCRelative Cell Count13413.0%
13.013.0%2022-05-25
11123GT3C1250RPDRelative Population Doubling1347.9%
7.97.9%2022-05-25
12123GT4C1250-Count1MNCEMicronucleated Cells326620

2020
2022-05-25
13123GT5C1250-Count2MNCEMicronucleated Cells219017

1717
2022-05-25
14123GT6C1250-Count3MNCEMicronucleated Cells275813

1313
2022-05-25
15123GT7C1250-Count4MNCEMicronucleated Cells271421

2121
2022-05-25
16123GT8C1250MNCECE

Micronucleated Cells/Total Cells


0.66%
0.660.66%2022-05-25
Expand
titlete.xpt (trial elements)
RowSTUDYIDASSAYIDDOMAINETCDELEMENT
Expand
titleta.xpt (trial arms)
RowSTUDYIDASSAYIDDOMAINARMCDARMTAETORDETCDELEMENT
Expand
titleei.xpt (dm-like)

Not needed.

RowSTUDYIDDOMAINENID (Entity ID)RICCRCCRPDSum of cell ev.Cells with MNSMKFID (Smoke Fraction)

REPLCTID

(Replicate Number)

PLATEID (Plate ID)

COLID

(Column number)

ROWID (Row  number)SETCD (Set Code, TX)RFSTDTCRFENDTCRFXSTDTCRFXENDTCRFCSTDTCRFCENDTC